public interface JmolBioModelSet
Modifier and Type | Method and Description |
---|---|
void |
calcAllRasmolHydrogenBonds(BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
BS bsHBonds) |
void |
calcSelectedMonomersCount() |
void |
calculateAllPolymers(Group[] groups,
int groupCount,
int baseGroupIndex,
BS modelsExcluded) |
java.lang.String |
calculateAllStructuresExcept(BS alreadyDefined,
boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha) |
java.lang.String |
calculateAllStuctures(BS bsAtoms,
boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
void |
calculateStraightnessAll() |
int |
calculateStruts(BS bs1,
BS bs2) |
java.lang.String |
getAllDefaultStructures(BS bsAtoms,
BS bsModified) |
java.util.Map<java.lang.String,java.lang.String> |
getAllHeteroList(int modelIndex) |
void |
getAllPolymerInfo(BS bs,
java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info) |
void |
getAllPolymerPointsAndVectors(BS bs,
javajs.util.Lst<javajs.util.P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
BS |
getAllSequenceBits(java.lang.String specInfo,
BS bsAtoms,
BS bsResult) |
BS |
getAtomBitsBS(int tokType,
BS bsInfo,
BS bs) |
BS |
getAtomBitsStr(int tokType,
java.lang.String specInfo,
BS bs) |
int |
getBioPolymerCountInModel(int modelIndex) |
java.lang.String |
getFullProteinStructureState(BS bsAtoms,
int mode) |
BS |
getGroupsWithinAll(int nResidues,
BS bs) |
BS |
getIdentifierOrNull(java.lang.String identifier) |
boolean |
mutate(BS bs,
java.lang.String group,
java.lang.String[] sequence) |
void |
recalculateAllPolymers(BS bsModelsExcluded,
Group[] groups) |
void |
recalculatePoints(int modelIndex) |
void |
setAllConformation(BS bsAtoms) |
void |
setAllProteinType(BS bs,
STR type) |
void |
setAllStructureList(java.util.Map<STR,float[]> structureList) |
void calcAllRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
void calcSelectedMonomersCount()
void calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)
java.lang.String calculateAllStuctures(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
java.lang.String calculateAllStructuresExcept(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
void calculateStraightnessAll()
java.util.Map<java.lang.String,java.lang.String> getAllHeteroList(int modelIndex)
void getAllPolymerPointsAndVectors(BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
int getBioPolymerCountInModel(int modelIndex)
java.lang.String getFullProteinStructureState(BS bsAtoms, int mode)
BS getIdentifierOrNull(java.lang.String identifier)
boolean mutate(BS bs, java.lang.String group, java.lang.String[] sequence)
void recalculatePoints(int modelIndex)
void setAllConformation(BS bsAtoms)
void setAllStructureList(java.util.Map<STR,float[]> structureList)
void getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info)